# | Line 36 | Line 36 | |
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36 | * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). | |
37 | * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). | |
38 | * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). | |
39 | < | * [4] Vardeman & Gezelter, in progress (2009). |
39 | > | * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
40 | > | * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
41 | */ | |
42 | ||
43 | #ifndef PARALLEL_FORCEDECOMPOSITION_HPP | |
# | Line 45 | Line 46 | |
46 | #include "brains/SimInfo.hpp" | |
47 | #include "brains/SnapshotManager.hpp" | |
48 | #include "nonbonded/NonBondedInteraction.hpp" | |
49 | + | #include "nonbonded/Cutoffs.hpp" |
50 | + | #include "nonbonded/InteractionManager.hpp" |
51 | + | #include "utils/Tuple.hpp" |
52 | ||
53 | using namespace std; | |
54 | namespace OpenMD { | |
55 | ||
56 | + | typedef tuple3<RealType, RealType, RealType> groupCutoffs; |
57 | + | |
58 | /** | |
59 | * @class ForceDecomposition | |
60 | * | |
# | Line 86 | Line 92 | namespace OpenMD { | |
92 | class ForceDecomposition { | |
93 | public: | |
94 | ||
95 | < | ForceDecomposition(SimInfo* info); |
95 | > | ForceDecomposition(SimInfo* info, InteractionManager* iMan); |
96 | virtual ~ForceDecomposition() {} | |
97 | ||
98 | virtual void distributeInitialData() = 0; | |
99 | virtual void distributeData() = 0; | |
100 | + | virtual void zeroWorkArrays() = 0; |
101 | virtual void collectIntermediateData() = 0; | |
102 | virtual void distributeIntermediateData() = 0; | |
103 | virtual void collectData() = 0; | |
104 | + | virtual potVec* getEmbeddingPotential() { return &embeddingPot; } |
105 | + | virtual potVec* getPairwisePotential() { return &pairwisePot; } |
106 | ||
107 | // neighbor list routines | |
108 | virtual bool checkNeighborList(); | |
109 | virtual vector<pair<int, int> > buildNeighborList() = 0; | |
110 | ||
111 | + | // how to handle cutoffs: |
112 | + | void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;} |
113 | + | void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; } |
114 | + | |
115 | // group bookkeeping | |
116 | < | virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0; |
116 | > | virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0; |
117 | > | virtual Vector3d getGroupVelocityColumn(int atom2) = 0; |
118 | ||
119 | // Group->atom bookkeeping | |
120 | virtual vector<int> getAtomsInGroupRow(int cg1) = 0; | |
# | Line 116 | Line 130 | namespace OpenMD { | |
130 | virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0; | |
131 | ||
132 | // atom bookkeeping | |
133 | < | virtual vector<int> getAtomList() = 0; |
134 | < | virtual vector<int> getSkipsForAtom(int atom1) = 0; |
133 | > | virtual int getNAtomsInRow() = 0; |
134 | > | virtual vector<int> getExcludesForAtom(int atom1) = 0; |
135 | virtual bool skipAtomPair(int atom1, int atom2) = 0; | |
136 | + | virtual bool excludeAtomPair(int atom1, int atom2) = 0; |
137 | + | virtual int getTopologicalDistance(int atom1, int atom2) = 0; |
138 | virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0; | |
139 | virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0; | |
140 | + | virtual Vector3d getAtomVelocityColumn(int atom2) = 0; |
141 | ||
142 | // filling interaction blocks with pointers | |
143 | < | virtual InteractionData fillInteractionData(int atom1, int atom2) = 0; |
144 | < | virtual InteractionData fillSkipData(int atom1, int atom2) = 0; |
145 | < | virtual SelfData fillSelfData(int atom1); |
143 | > | virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
144 | > | virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
145 | > | |
146 | > | virtual void fillSelfData(SelfData &sdat, int atom1); |
147 | > | |
148 | > | virtual void addToHeatFlux(Vector3d hf); |
149 | > | virtual void setHeatFlux(Vector3d hf); |
150 | ||
151 | protected: | |
152 | SimInfo* info_; | |
153 | SnapshotManager* sman_; | |
154 | Snapshot* snap_; | |
155 | + | ForceField* ff_; |
156 | + | InteractionManager* interactionMan_; |
157 | + | |
158 | int storageLayout_; | |
159 | + | bool needVelocities_; |
160 | RealType skinThickness_; /**< Verlet neighbor list skin thickness */ | |
161 | + | RealType largestRcut_; |
162 | ||
163 | < | map<pair<int, int>, int> topoDist; //< topoDist gives the |
164 | < | //topological distance between |
165 | < | //two atomic sites. This |
140 | < | //declaration is agnostic |
141 | < | //regarding the parallel |
142 | < | //decomposition. The two |
143 | < | //indices could be local or row |
144 | < | //& column. It will be up to |
145 | < | //the specific decomposition |
146 | < | //method to fill this. |
147 | < | map<pair<int, int>, bool> exclude; //< exclude is the set of pairs |
148 | < | //to leave out of non-bonded |
149 | < | //force evaluations. This |
150 | < | //declaration is agnostic |
151 | < | //regarding the parallel |
152 | < | //decomposition. The two |
153 | < | //indices could be local or row |
154 | < | //& column. It will be up to |
155 | < | //the specific decomposition |
156 | < | //method to fill this. |
163 | > | vector<int> idents; |
164 | > | potVec pairwisePot; |
165 | > | potVec embeddingPot; |
166 | ||
167 | + | /** |
168 | + | * The topological distance between two atomic sites is handled |
169 | + | * via two vector structures for speed. These structures agnostic |
170 | + | * regarding the parallel decomposition. The index for |
171 | + | * toposForAtom could be local or row, while the values could be |
172 | + | * local or column. It will be up to the specific decomposition |
173 | + | * method to fill these. |
174 | + | */ |
175 | + | vector<vector<int> > toposForAtom; |
176 | + | vector<vector<int> > topoDist; |
177 | + | vector<vector<int> > excludesForAtom; |
178 | vector<vector<int> > groupList_; | |
179 | + | vector<RealType> massFactors; |
180 | + | vector<AtomType*> atypesLocal; |
181 | + | |
182 | vector<Vector3i> cellOffsets_; | |
183 | Vector3i nCells_; | |
184 | vector<vector<int> > cellList_; | |
185 | vector<Vector3d> saved_CG_positions_; | |
186 | ||
187 | + | bool userChoseCutoff_; |
188 | + | RealType userCutoff_; |
189 | + | CutoffPolicy cutoffPolicy_; |
190 | + | |
191 | + | map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap; |
192 | + | |
193 | }; | |
194 | } | |
195 | #endif |
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